Análisis de introgresión en Apis mellifera iberiensis y Apis mellifera mellifera usando polimorfismos de nucleótidos simples (SNPs)

Diferentes estudios han agrupado las subespecies de A. mellifera en cuatro linajes evolutivos basados sobre marcadores morfométricos, ecológicos, microsatélites y mtDNA: Africano (A), Medio Oriente (O), Este y Centro de Europa (C), Norte y Oeste de Europa (M). El linaje M está representado por las subespecies A. m. iberiensis y A. m. mellifera, cuya distribución es la Península Ibérica para la primera y desde los Pirineos hacia el Norte de Europa para la segunda. Durante las últimas décadas, la introducción masiva de subespecies del linaje C por apicultores ha ocasionado un fuerte flujo génico y más aún al casi completo remplazamiento de A. m. mellifera, como ha sido reportado para Alemania. Por tanto, el análisis de niveles de introgresión en programas de crianza y conservación es de vital importancia para evitar la perdida de diversidad genética y sustitución de especies nativas. Este estudio busca identificar los niveles de introgresión de subespecies del linaje C en las subespecies pertenecientes al linaje M a través de un análisis amplio del genoma usando SNPs. Para 711 individuos correspondiente a A. m. iberiensis y 88 individuos A. m. mellifera fueron genotipados 1536 SNPs. Las subespecies de linaje C A. m. ligustica y A. m. carnica fueron usados como poblaciones de referencia. Los niveles de introgresión fueron evaluados usando un método de agrupamiento Bayesiano implementado en el software STRUCTURE. Nuestros resultados indicaron que la introgresión en A. m .iberiensis no es significante, a diferencia en A. m. mellifera que presentó de 8% a 30% de introgresión. Considerando que muchas de las muestras de A. m. mellifera son provenientes de poblaciones integradas en programas de conservación en el Norte de Europa, este resultado evidencia el profundo contraste entre las dos subespecies del linaje M con respecto a su estado de conservación

Reduced SNP panels for genetic identification and introgression analysis in the dark honey bee (Apis mellifera mellifera)

Beekeeping activities, especially queen trading, have shaped the distribution of honey bee (Apis mellifera) subspecies in Europe, and have resulted in extensive introductions of two eastern European C-lineage subspecies (A. m. ligustica and A. m. carnica) into the native range of the M-lineage A. m. mellifera subspecies in Western Europe. As a consequence, replacement and gene flow between native and commercial populations have occurred at varying levels across western European populations. Genetic identification and introgression analysis using molecular markers is an important tool for management and conservation of honey bee subspecies. Previous studies have monitored introgression by using microsatellite, PCR-RFLP markers and most recently, high density assays using single nucleotide polymorphism (SNP) markers. While the latter are almost prohibitively expensive, the information gained to date can be exploited to create a reduced panel containing the most ancestry-informative markers (AIMs) for those purposes with very little loss of information. The objective of this study was to design reduced panels of AIMs to verify the origin of A. m. mellifera individuals and to provide accurate estimates of the level of C-lineage introgression into their genome. The discriminant power of the SNPs using a variety of metrics and approaches including the Weir & Cockerham's FST, an FST-based outlier test, Delta, informativeness (In), and PCA was evaluated. This study shows that reduced AIMs panels assign individuals to the correct origin and calculates the admixture level with a high degree of accuracy. These panels provide an essential tool in Europe for genetic stock identification and estimation of admixture levels which can assist management strategies and monitor honey bee conservation programs

Spatial patterns of single nucleotide polymorphisms (SNPs) support a scenario of secondary contact in Iberian honey bees (Apis mellifera iberiensis)

Dissecting diversity patterns of organisms endemic to Iberia has been truly challenging for a variety of plant and animal taxa, and the Iberian honey bee (A. m. iberiensis) is no exception. Here we used a genome-wide data set of 309 neutrally-tested SNPs, scattered across the 16 honey bee chromosomes, which were genotyped in 711 honey bee individuals. These SNPs were analyzed along with an intergenic locus of the mtDNA. The two markers revealed the existence of a strong and concordant structure supporting a process of secondary contact.We owe special thanks to beekeepers from Spain and Portugal for their valuable help in obtaining samples. Antonio Pajuelo provided the contacts of Spanish beekeepers. DNA extraction and SNP genotyping were performed by Colette Abbey. Special thanks to Margarida Neto, Andreia Brandão and Irene Muñoz for collaborating in the sampling. JC-G and DH are supported by Fundação para a Ciência e Tecnologia (FCT) through the scholarships SFRH/BD/68682/2010 and SFRH/BD/84195/2012, respectively. This research was funded by FCT and COMPETE/QREN/EU through the project PTDC/BIA-BEC/099640/2008 and BiodivERsA-FACCE2014-91.info:eu-repo/semantics/publishedVersio

Inferência da estrutura populacional de Apis mellifera iberiensis utilizando marcadores nucleares (polimorfismo de nucleótido simples, SNP) e mitocondrial

A Península Ibérica alberga a maior complexidade e diversidade da abelha melífera na Europa, pelo que desvendar a história evolutiva da subespécie Apis mellifera iberiensis é um desafio. Com o objectivo de decifrar quais os mecanismos subjacentes a esta diversidade, diversos estudos têm sido efectuados. Estudos iniciais usando a morfologia e alozimas mostraram a existência de um gradiente desde África até ao Norte de Europa, sendo as abelhas ibéricas caracterizadas como tendo um fenótipo intermédio. Por outro lado, a análise do mtDNA indicou a co‐ocorrência de duas linhagens divergentes (Africana, A, e Norte Europeia, M)) formando um cline com orientação sudoeste ‐ nordeste. Estes dois padrões levaram os cientistas a proporem duas hipóteses para explicar a origem da abelha ibérica. Enquanto a primeira hipótese, baseada na morfologia e alozimas, defende um processo de intergradação primária, a segunda hipótese, usando o mtDNA, defende um contacto secundário recente entre populações do norte de África e da Península Ibérica. Por outro lado, os microsatélites não suportam nenhuma das hipóteses. Numa tentativa de resolver este debate efectuou‐se uma amostragem constituída por 711 indivíduos distribuídos ao longo de três transeptos na Península Ibérica. Estes indivíduos foram genotipados usando tanto marcadores nucleares (polimorfismo de nucleótido simples, SNP) como (região tRNAleu‐ cox2 do mtDNA). Diversas análises foram efectuadas usando ferramentas bioinformáticas de genética populacional e de genética da paisagem. Os resultados dos dois marcadores utilizados são concordantes, recuperando cline sudoeste‐nordeste. No entanto, os níveis de diferenciação entre as populações Ibéricas e as do Norte de África não suportam um contacto secundário recente.Fundação para a Ciência e Tecnologi

Padrões de variação materna da abelha Ibérica: um estudo de fina resolução espacial

Estudos prévios usando diferentes marcadores do ADN mitocondrial sugerem que a Península Ibérica tem sido uma área de contacto secundário natural entre duas linhagens divergentes de abelhas (linhagem Africana e linhagem da Europa ocidental) formando um cline com orientação sudoeste-nordeste. Porém, é provável que com a crescente intensificação da actividade apícola haja uma alteração do padrão de diversidade moldado pelas forças evolutivas ao longo de milhares de anos. Nesta comunicação o padrão de variação materna é representado espacialmente usando dados de sequenciação da região intergénica tRNAleu-cox2 do mtDNA obtidos para 711 colónias recentemente amostradas ao longo de três transeptos com orientação norte-sul (costa Atlântica, região central e costa Mediterrânica). Este estudo constitui a mais recente e completa representação espacial da diversidade materna à escala de toda Península Ibérica permitindo uma avaliação da influência dos processos antropogénicos (como por exemplo transumância e introdução de rainhas exóticas) na composição genética materna da abelha ibérica.Fundação para a Ciência e Tecnologi

Effect of linkage disequilibrium on inferences of population structure and introgression of iberian and black honey bees

Identification of population structure, a primary goal in population genetics, is easily performed because there is a number of methods available, implemented by user-friendly software packages. However, the user must be cautious when inferring population structure because spurious results may be obtained when there is strong linkage disequilibrium. With recent development of high-density SNPs we have now more power to interrogate the honey bee genome. However, the greater the number of loci genotyped the greater the chance of scoring loci that are linked. In addition, events such as population bottleneck, small effective population size, genetic drift, and admixture may also generate strong linkage disequilibrium. According to Kaeuffer et al. (2007), correlation rLD is the best way to deal with linkage disequilibrium. These authors recommend removing loci with rLD higher than 0.5 when inferring structure. In this study we used the GoldenGate Assay of Illumina to genotype over 1221 loci in individuals sampled from populations of A.m. iberiensis and A.m. mellifera. In this dataset we used the genetic distance between SNPs and rLD to test the effect of linkage in the number of clusters and the introgression level inferred by the clustering method implemented in the software STRUCTURE.Fundação para a Ciência e Tecnologi

SNPs selected by information content outperform randomly selected microsatellite loci for delineating genetic identification and introgression in the endangered dark European honeybee (Apis mellifera mellifera)

The honeybee (Apis mellifera) has been threatened by multiple factors including pests and pathogens, pesticidesand loss of locally adapted gene complexes due to replacement and introgression. In western Europe, the geneticintegrity of the native A. m. mellifera (M-lineage) is endangered due to trading and intensive queen breeding withcommercial subspecies of eastern European ancestry (C-lineage). Effective conservation actions require reliablemolecular tools to identify pure-bred A. m. mellifera colonies. Microsatellites have been preferred for identificationof A. m. mellifera stocks across conservation centres. However, owing to high throughput, easy transferabilitybetween laboratories and low genotyping error, SNPs promise to become popular. Here, we compared the resolvingpower of a widely utilized microsatellite set to detect structure and introgression with that of different sets that com-bine a variable number of SNPs selected for their information content and genomic proximity to the microsatelliteloci. Contrary to every SNP data set, microsatellites did not discriminate between the two lineages in the PCA space.Mean introgression proportions were identical across the two marker types, although at the individual level,microsatellites’ performance was relatively poor at the upper range of Q-values, a result reflected by their lower pre-cision. Our results suggest that SNPs are more accurate and powerful than microsatellites for identification of A. m.mellifera colonies, especially when they are selected by information content.info:eu-repo/semantics/publishedVersio

Wing geometric morphometrics of workers and drones and single nucleotide polymorphisms provide similar genetic structure in the Iberian honey bee (Apis mellifera iberiensis)

Wing geometric morphometrics has been applied to honey bees (Apis mellifera) in identification of evolutionary lineages or subspecies and, to a lesser extent, in assessing genetic structure within subspecies. Due to bias in the production of sterile females (workers) in a colony, most studies have used workers leaving the males (drones) as a neglected group. However, considering their importance as reproductive individuals, the use of drones should be incorporated in these analyses in order to better understand diversity patterns and underlying evolutionary processes. Here, we assessed the usefulness of drone wings, as well as the power of wing geometric morphometrics, in capturing the signature of complex evolutionary processes by examining wing shape data, integrated with geographical information, from 711 colonies sampled across the entire distributional range of Apis mellifera iberiensis in Iberia. We compared the genetic patterns reconstructed fromspatially-explicit shape variation extracted fromwings of both sexes with that previously reported using 383 genome-wide SNPs (single nucleotide polymorphisms). Our results indicate that the spatial structure retrieved from wings of drones and workers was similar (r = 0.93) and congruent with that inferred from SNPs (r = 0.90 for drones; r = 0.87 for workers), corroborating the clinal pattern that has been described for A. m. iberiensis using other genetic markers. In addition to showing that drone wings carry valuable genetic information, this study highlights the capability of wing geometric morphometrics in capturing complex genetic patterns, o ering a reliable and low-cost alternative for preliminary estimation of population structure.This research was funded by the program COMPETE 2020—POCI (Programa Operacional para a Competividade e Internacionalização) and by Portuguese funds through FCT (Fundação para a Ciência e a Tecnologia) in the framework of the project BeeHappy (POCI-01-0145-FEDER-029871). FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo) provided funds for TMF (2011/07857-9) and JSGT (2011/02434-2).info:eu-repo/semantics/publishedVersio

Signatures of selection in the Iberian honey bee: a genome wide approach using single nucleotide polymorphisms (SNPs)

Dissecting genome-wide (expansions, contractions, admixture) from genome-specific effects (selection) is a goal of central importance in evolutionary biology because it leads to more robust inferences of demographic history and to identification of adaptive divergence. The publication of the honey bee genome and the development of high-density SNPs genotyping, provide us with powerful tools, allowing us to identify signatures of selection in the honey bee genome. These signatures will be an important first step towards understanding the transition of genotype into phenotype and the basis of adaptive divergence. The Iberian Peninsula harbours the greatest honey bee genetic diversity and complexity in Europe. The challenge of deciphering the mechanisms underlying such complexity has led to numerous morphological and molecular marker-based surveys of the Iberian honey bee. Yet, in spite of the numerous studies, the evolutionary processes underlying patterns of Iberian honey bee genetic diversity remain poorly understood. The evolutionary process in the Iberian Peninsula has been dynamic and the genetic consequences are too complex to be addressed piecemeal, using few markers with unknown or poorly known linkage relationships. Accordingly, in 2010 more than 650 honey bee colonies were sampled across latitudinal and longitudinal clines in the Iberian Peninsula. The 650 honey bee samples were genotyped for 1536 SNPs – all equally distributed across the honey bee genome and all with known linkage relationships, based on the latest honey bee genome assembly. Herein we show the preliminary results of this genotyping, focusing on an Iberian honey bee genome inquiry on recent selective sweeps. We provide new insights into the evolutionary processes shaping the Iberian honey bee patterns

Does geometric morphometrics provide congruent results with SNP data? The case of Iberian honey bee (Apis mellifera iberiensis)

While molecular markers are usually preferred to infer population structure, geometric morphometrics is a cheap method that has been widely applied to the wings of female honey bees to identify subspecies or lineages and can be used alternatively or complementarily to molecular markers. However, the power of geometric morphometrics to capture the signature of complex evolutionary processes has not been tested in honey bees. In this study, we applied geometric morphometrics, combined with geographical information, to the right forewings of female individuals from 711 colonies distributed along the Iberian Peninsula, which contains a complex population structure. The results were further compared with those obtained using 383 SNPs. Our data showed that geometric morphometrics provided a similar spatial structure of SNPs data (r=0.90). Our findings reinforce the power of spatially explicit wing geometric morphometrics data to capture the signature of complex evolutionary processes. Thus, this method could be used as a low-cost alternative for preliminary estimation of population structure.info:eu-repo/semantics/publishedVersio